TY  - JOUR
AU  - Mehta, Subina
AU  - Bernt, Matthias
AU  - Chambers, Matthew
AU  - Fahrner, Matthias
AU  - Föll, Melanie Christine
AU  - Gruening, Bjoern
AU  - Horro, Carlos
AU  - Johnson, James E
AU  - Loux, Valentin
AU  - Rajczewski, Andrew T
AU  - Schilling, Oliver
AU  - Vandenbrouck, Yves
AU  - Gustafsson, Ove Johan Ragnar
AU  - Thang, W C Mike
AU  - Hyde, Cameron
AU  - Price, Gareth
AU  - Jagtap, Pratik D
AU  - Griffin, Timothy J
TI  - A Galaxy of informatics resources for MS-based proteomics.
JO  - Expert review of proteomics
VL  - 20
IS  - 11
SN  - 1478-9450
CY  - Abingdon
PB  - Taylor & Francis Group
M1  - DKFZ-2023-01999
SP  - 251-266
PY  - 2023
N1  - 2023 Jul-Dec;20(11):251-266
AB  - Continuous advances in mass spectrometry (MS) technologies have enabled deeper and more reproducible proteome characterization, and a better understanding of biological systems when integrated with other 'omics data. Bioinformatic resources meeting analysis requirements of increasingly complex MS-based proteomic data, and associated multi-omic data, are critically needed. These requirements included availability of software spanning diverse types of analyses, along with scalability for large-scale, compute-intensive applications and mechanisms to ease adoption of the software.The Galaxy ecosystem meets these requirements by offering a multitude of open-source tools for MS-based proteomics analyses and applications, all in an adaptable, scalable, and accessible computing environment. A thriving global community maintains these software and associated training resources to empower researcher-driven analyses.The community-supported Galaxy ecosystem remains a crucial contributor to basic biological and clinical studies using MS-based proteomics. In addition to the current status of Galaxy-based resources, we describe ongoing developments for meeting emerging challenges in MS-based proteomic informatics. We hope this review will catalyze increased use of Galaxy by researchers employing MS-based proteomics and inspire software developers to join the community and implement new tools, workflows, and associated training content that will add further value to this already rich ecosystem.
KW  - Bioinformatics (Other)
KW  - Computational workflows (Other)
KW  - Galaxy platform (Other)
KW  - Mass-spectrometry (Other)
KW  - Multi-omics (Other)
KW  - Reproducibility (Other)
KW  - proteomics (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:37787106
DO  - DOI:10.1080/14789450.2023.2265062
UR  - https://inrepo02.dkfz.de/record/284410
ER  -